Depletion-assisted multiplexed cell-free RNA sequencing reveals distinct human and microbial signatures in plasma versus extracellular vesicles.

Background: Cell-free long RNAs in human plasma and extracellular vesicles (EVs) have shown promise as biomarkers in liquid biopsy, despite their fragmented nature.

Methods: To investigate these fragmented cell-free RNAs (cfRNAs), we developed a cost-effective cfRNA sequencing method called DETECTOR-seq (depletion-assisted multiplexed cell-free total RNA sequencing). DETECTOR-seq utilised a meticulously tailored set of customised guide RNAs to remove large amounts of unwanted RNAs (i.

Cell-free multi-omics analysis reveals potential biomarkers in gastrointestinal cancer patients' blood.

During cancer progression, tumorigenic and immune signals are spread through circulating molecules, such as cell-free DNA (cfDNA) and cell-free RNA (cfRNA) in the blood. So far, they have not been comprehensively investigated in gastrointestinal cancers. Here, we profile 4 categories of cell-free omics data from patients with colorectal cancer and patients with stomach adenocarcinoma and then assay 15 types of genomic, epigenomic, and transcriptomic variations.

Cell-free RNA for the liquid biopsy of gastrointestinal cancer.

Gastrointestinal (GI) cancer includes many cancer types, such as esophageal, liver, gastric, pancreatic, and colorectal cancer. As the cornerstone of personalized medicine for GI cancer, liquid biopsy based on noninvasive biomarkers provides promising opportunities for early diagnosis and dynamic treatment management. Recently, a growing number of studies have demonstrated the potential of cell-free RNA (cfRNA) as a new type of noninvasive biomarker in body fluids, such as blood, saliva, and urine.

Identification of novel cell-free RNAs in maternal plasma as preterm biomarkers in combination with placental RNA profiles.

Background: Preterm birth (PTB) is the main driver of newborn deaths. The identification of pregnancies at risk of PTB remains challenging, as the incomplete understanding of molecular mechanisms associated with PTB. Although several transcriptome studies have been done on the placenta and plasma from PTB women, a comprehensive description of the RNA profiles from plasma and placenta associated with PTB remains lacking.

Identification and Evaluation of Recombinant Outer Membrane Proteins as Vaccine Candidates Against .

found in the normal flora of the human oral and intestinal tract mainly causes hospital-acquired infections but can also cause community-acquired infections. To date, most clinical trials of vaccines against have ended in failure. Furthermore, no single conserved protein has been identified as an antigen candidate to accelerate vaccine development.

Integrative analysis of long extracellular RNAs reveals a detection panel of noncoding RNAs for liver cancer.

Long extracellular RNAs (exRNAs) in plasma can be profiled by new sequencing technologies, even with low abundance. However, cancer-related exRNAs and their variations remain understudied. We investigated different variations (i.

Screening of Polyvalent Phage-Resistant Strains Based on Phage Receptor Analysis.

Bacteria-based biotechnology processes are constantly under threat from bacteriophage infection, with phage contamination being a non-neglectable problem for microbial fermentation. The essence of this problem is the complex co-evolutionary relationship between phages and bacteria. The development of phage control strategies requires further knowledge about phage-host interactions, while the widespread use of strain BL21 (DE3) in biotechnological processes makes the study of phage receptors in this strain particularly important.

Identification of a lytic Pseudomonas aeruginosa phage depolymerase and its anti-biofilm effect and bactericidal contribution to serum.

Pseudomonas aeruginosa (P. aeruginosa) infection has imposed a great threat to patients with cystic fibrosis. With the emergence of multidrug-resistant P.

Genomic and biological characterization of the Vibrio alginolyticus-infecting "Podoviridae" bacteriophage, vB_ValP_IME271.

As an opportunist pathogen, Vibrio alginolyticus (V. alginolyticus), causes disease in marine animals. Bacterial contamination of seafood is not uncommon, and phage therapy is considered a safe way to decontaminate such foods to control the emergence of vibriosis.

Characterization and genome analysis of novel phage vB_EfaP_IME195 infecting Enterococcus faecalis.

Enterococcus faecalis is one of the main bacteria in the human and animal intestine but is also classed as an opportunistic pathogen. During normal growth, E. faecalis produces natural antibiotics and is conducive to human health.

Isolation and characterization of a novel phage Xoo-sp2 that infects Xanthomonas oryzae pv. oryzae.

Bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a serious bacterial disease in rice-growing regions worldwide. Phage therapy has been proposed as a potential measure to treat bacterial infections.

Investigation on Mosquito-Borne Viruses at Lancang River and Nu River Watersheds in Southwestern China.

During 2007 and 2010, an extensive entomological survey was performed to assess the distribution of mosquitoes and mosquito-borne arboviruses at Lancang River and Nu River watersheds in southwestern China. A total of 20,450 mosquitoes consisting 20 species was trapped and submitted 261 pools according to species and location. Culex tritaeniorhynchus and Anopheles sinensis were the most abundant species.

Complete genome sequence of a novel, virulent Ahjdlikevirus bacteriophage that infects Enterococcus faecium.

A novel virulent bacteriophage named vB_EfaP_IME199 that specifically infects Enterococcus faecium was isolated and characterized. Its optimal multiplicity of infection was 0.01, and it had a 30 minute outbreak period.

Complete Genome Sequence of a Novel Multidrug-Resistant Phage, vB_Kpn_IME260.

is the most common clinically important opportunistic bacterial pathogen and its infection is often iatrogenic. Its drug resistance poses a grave threat to public health. The genomic data reported here comprise an important resource for research on phage therapy in the control of drug-resistant bacteria.

Characterization and complete genome sequence analysis of a novel virulent Siphoviridae phage against Staphylococcus aureus isolated from bovine mastitis in Xinjiang, China.

Bovine mastitis is one of the most costly diseases in dairy cows worldwide. It can be caused by over 150 different microorganisms, where Staphylococcus aureus is the most frequently isolated and a major pathogen responsible for heavy economic losses in dairy industry. Although antibiotic therapy is most widely used, alternative treatments are necessary due to the increasing antibiotic resistance.

First complete genome sequence of a virulent bacteriophage infecting the opportunistic pathogen Serratia rubidaea.

A Serratia rubidaea phage, vB_Sru IME250, was isolated from hospital sewage. The morphology suggested that phage vB_Sru IME250 should be classified as a member of the family Myoviridae. High-throughput sequencing revealed that the phage genome has 154,938 nucleotides and consists of 193 coding DNA sequences, 90 of which have putative functions.

A novel mosquito-borne reassortant orbivirus isolated from Xishuangbanna, China.

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Electronic Supplementary Material: Supplementary material is available for this article at 10.1007/s12250-016-3886-2 and is accessible for authorized users.

Complete Genome Sequence of a New Enterococcus faecalis Bacteriophage, vB_EfaS_IME197.

We report here the whole-genome sequence of a new Enterococcus faecalis phage, vB_EfaS_IME197, which has a linear double-stranded DNA genome of 41,307 bp with 34% G+C content. We describe the main features of the genome of vB_EfaS_IME197.